The wind howls down a bleak street in Croatia's Borovo Naselje, lashing the rain against the garage door that Sinisa Mihajlovic's father had to replace every few weeks because of the force with which his son practised his free-kicks against it. It is not just the garage door that has been replaced. The whole house was destroyed during the Yugoslav war. Mihajlovic, wonderful and controversial footballer and now manager of Serbia, is defined by the war, adding another layer of complexity to the already incendiary meeting between Croatia and Serbia in World Cup qualifying on Friday night.

Borovo Naselje lies between Vukovar, a name emblematic of the atrocities of the war that tore Yugoslavia apart in the early 1990s, and Borovo Selo, where the first ordnance of the war was fired. In 1991 the area was besieged by the Yugoslav National Army and Serbian paramilitaries, eventually falling after three months. All the inhabitants of the town were rounded up, irrespective of ethnicity, and taken to camps in Serbia. One of those captured was Zvonko Popovic, the coach of Borovo when Mihajlovic made his debut with the team, aged 17, in 1986. He was released a month later when it turned out one of the colonels guarding the camp was a fan of the footballer Mile Stamenkovic, who had been Popovic's best man.

It is not entirely clear but it seems probable the Mihajlovic house was destroyed during the siege. When Croatian forces retook the town, a childhood friend of Mihajlovic's, a Croat, told of how he was forced to shoot at photographs of his old schoolmate to prove he was committed to the Croatian cause. The scars of the conflict are still clear: some houses still lie in ruins, others are pocked by bullet-holes. The pitch at Borovo's stadium, once considered the best in Yugoslavia, is bumpy, the grass unkempt. Mihajlovic, his childhood friend Sinisa Lazic said, cannot return home. "Normally, if people saw a footballer in the street – [Nemanja] Vidic, [Edin] Dzeko, whoever – they'd shake their hand and wish them good luck," he said. "Not Sinisa."

He has come to be considered an icon of Serbian nationalism but Mihajlovic's is a complicated history. His father was a Serb, his mother a Croat. He very nearly joined Dinamo Zagreb in 1987, turning them down in a fit of stubbornness because – he claimed in his autobiography – he was told by Mirko Jovic, the Croatian coach of the Yugoslavia Under-20 side, that he would be selected for the youth World Cup only if he signed. Things may have turned out very differently had he moved to Zagreb; as it was, he moved to Vojvodina Novi Sad and then to Belgrade where he played for Crvena Zvezda (Red Star).

In his first season at the club, 1990-91, Zvezda won the European Cup. Mihajlovic scored the opening goal in the second leg of the semi-final against Bayern Munich, a game that ended in 20 of the most astonishing minutes of football ever played and, after a last-minute own-goal from Klaus Augenthaler had won it for Zvezda, a mass pitch invasion.

Serbian volunteers load a cannon on the front line during the fighting for Vukovar against Croatian forces in Borovo Selo in October 1991. Photograph: Marja Illic/AFP/Getty Images

It was a celebration and yet something more; as fans tore up the pitch for souvenirs, it seemed an acknowledgment that it would not be needed any more; the incident in Borovo Selo, which led to fatalities on both sides, happened between the two legs of the semi-final.

A week later Zvezda played Hajduk Split in the Yugoslav cup final. Hajduk won 1-0 but the game was at least as notable for the clash between Mihajlovic and Igor Stimac, now the coach of Croatia. "In one moment we were face to face," Mihajlovic later revealed. "He leaned to me and said, his voice full of hatred, 'I pray to God your whole family in Borovo gets murdered!' At that moment I could have killed him with my teeth..." Mihajlovic made a series of bad fouls on Stimac and in the end both were sent off. Stimac and he have been sworn enemies ever since. "Here is a man who spread lies about me, such as that I was gay; he also said he could strangle me with his bare hands," Stimac said. "But his mother is Croatian, his wife Italian, he married and baptised his children in a Catholic [as opposed to Serb Orthodox] church. I realise he has to try twice as hard as anyone else there to prove his allegiance to Serbia – but they will never accept him, no matter how much he carries Arkan's picture around."

Both coaches have spent the last few days trying to play down their antipathy and insisting this is just another game. But even as he does so, Mihajlovic, now 44, admits that the fixture was one of the reasons he took the job of national manager and that he "would give three years of [his] life" to be playing in it. Those who knew him growing up in Borovo insist that is less for nationalistic reason than because of his intense competitiveness. "On the pitch, he'd spit on you and abuse you to win in the heat of the action," said Lazic, who played for Borovo and then for Hajduk Kula in the Serbian first division, "but that's the culture here. Sinisa on the pitch and Sinisa off the pitch are two different personalities."

Popovic made him Borovo's captain in the hope that the responsibility would calm him down, a tactic that was largely successful. Another friend, Sinisa Cuckovic, remembers the competitiveness extending beyond football. "He wanted to win at all sports and especially at school. He was very good at Serbo-Croatian language and literature. He was very confident and, if he hadn't succeeded in sport, he would have done in some other area. And the girls loved him."

His history teacher, Nebojsa Serbic, who also coached the school team, agrees Mihajlovic was "an excellent student, always sat at the front of the class". He remembers his "feistiness" but also speaks of the contrast between Mihajlovic the player and Mihajlovic the person. "I saw more talented players than him but none had his single-mindedness. He didn't drink, didn't smoke, nothing." Later he quit the best school in town to move to a poorer one because the times of lessons fitted better with his training.

Nothing about Mihajlovic is as simple as the stereotype of the snarling nationalist may make it seem. "Do you really think he can be nationalist like people say when his mother is a Croat?" Lazic asked. His relationship with the indicted war criminal Arkan, for instance, grew from the fact that Arkan protected him in Belgrade in the early 1990s when his dual ethnicity could have made things difficult.

Arkan also helped his parents flee Vukovar during the siege. Mihajlovic's uncle, his mother's brother, was a senior officer in the Croatian army and was taken prisoner after the fall of the town. Arkan called Mihajlovic and asked him to come and pick the uncle up before his men murdered him.

What people in Vukovar think about Mihajlovic is conditioned largely by ethnicity. "He was a hero here for everybody until '91," said Cuckovic. "If he'd gone to Dinamo and played for Croatia," Popovic said, "it would have been the Serbs who hated him. It's like a kind of jealousy."

Serbia, in its present form, has never played Croatia, although Yugoslavia – by then consisting of just Serbia and Montenegro – did play Croatia in qualifying for Euro 2000. The power failed at the first game in Belgrade, a 0-0 draw and when the lights came back on, it became clear that Yugoslav players had surrounded Croatia's players in the centre circle to protect them. In Zagreb, where a 2-2 draw eliminated Croatia, a huge banner commemorated "Vukovar 91"; Mihajlovic knelt before it and crossed himself, a gesture that was understandable in that he wanted to commemorate the fallen on both sides but one that was also hugely provocative, drawing a torrent of abuse from home fans.

There will be no away fans in the Maksimir. Police have threatened to stop the game if there is any nationalistic chanting and Mihajlovic has warned that any player who inflames the crowd will not be picked again. Lazic suggests his old team-mate has mellowed, "learned from his mistakes", but it is hard to imagine the complex figure of Mihajlovic will ever not be controversial.

"He's not a nationalist," said Serbic. "He's a patriot." Not many in Zagreb will be generous in making the distinction.